title: B73Ch1greenControl2

description:
Inbred lines B73 and Mo17, from the same stocks used to create the IBM mapping lines, were kindly supplied by M. Lee.  These lines were increased in the field nursery at Clayton, NC. Individual seeds were placed one per 6 cm pot filled with vermiculite, at a density of 36 pots per flat, and grown in the greenhouse without supplemental lighting for ten days to the two-leaf stage.  The greenhouse photosynthetically active radiation levels are ~20% less than outdoor radiation.  The two lines were then exposed to 4 h of ultraviolet radiation from UV313 bulbs (Q Panel, Westlake, OH, USA) suspended about 30 cm above the plants.  The UV dose was measured at plant height using the UV-B sensor on an International Light radiometer Model IL1400A (International Light, Newburyport, MA); the treatment plants received a total UV dose of 86 Jm-2.  Control plants were placed under UV313 bulbs that were covered with polyester (MylarD, US Plastics, Lima, OH, USA), which transmits visible light but excludes UV-B.  After UV irradiation the UV bulbs were turned off and the plants were allowed to recover for 4 h in the greenhouse.  The second and third seedling leaf from each of four plants was harvested and dropped immediately into liquid nitrogen.  Pooling assured sufficient RNA and also decreases biological variability.  Total RNA was extracted from frozen tissue using Trizol (Invitrogen Co., Carlsbad, CA), as described in the microarray manufacturer’s protocol (http://www.zmdb.iastate.edu/zmdb/microarray/protocols.html#P3).  PolyA-plus messenger RNA was prepared from the total RNA using a Qiagen Oligotex kit (Qiagen Corp., Valencia, CA).  Poly(A)+ RNA was isolated using Oligotex (Qiagen Inc., Valencia, CA), and 4 mg of poly (A)+ RNA was used for each cDNA synthesis using Superscript II reverse transcriptase (Life Technologies, Carlsbad, CA).  cDNA was labeled using 100 mM Cy5-dUTP or Cy3-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ).  Excess nucleotides and primers were removed using QIAquick PCR Purification Kit (Qiagen, Valencia, CA).  About 95% of the spotted cDNAs showed significant hybridization when leaf mRNA was used for the experiments.  The controlsample was labeled with Cy3-dUTP fluorescent dye and the UV treatment sample was labeled with Cy5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ, USA).  Two samples, one labeled with each dye, were mixed and then hybridized to a microarray for 15 h at 60°C.  The slides were washed in three wash steps: 2x SSC, 0.5% SDS; 0.5x SSC; and 0.05x SSC.  The three washes were at room temperature for 5 min each with gentle shaking.  The slides were scanned with a GenePix 4000B Scanner (Axon Instruments Inc., Union City, CA).  Normalization between the Cy3 and Cy5 fluorescent dye emission channels was achieved by adjusting the levels of both image intensities.  Scanalyze (Eisen, http://rana.lbl.gov/EisenSoftware.htm) was used to quantify the image files from the scanner.
Keywords = ultraviolet maize corn seedling leaf


title: B73Ch1greenUV1

status: Public on Sep 01 2004

type: RNA

city: Wilmington

first: Ann

last: Stapleton

state: NC

address: 601 S. College

department: Biological Sciences

country: USA

institute: University of North Carolina Wilmington

description:
Inbred lines B73 and Mo17, from the same stocks used to create the IBM mapping lines, were kindly supplied by M. Lee.  These lines were increased in the field nursery at Clayton, NC. Individual seeds were placed one per 6 cm pot filled with vermiculite, at a density of 36 pots per flat, and grown in the greenhouse without supplemental lighting for ten days to the two-leaf stage.  The greenhouse photosynthetically active radiation levels are ~20% less than outdoor radiation.  The two lines were then exposed to 4 h of ultraviolet radiation from UV313 bulbs (Q Panel, Westlake, OH, USA) suspended about 30 cm above the plants.  The UV dose was measured at plant height using the UV-B sensor on an International Light radiometer Model IL1400A (International Light, Newburyport, MA); the treatment plants received a total UV dose of 86 Jm-2.  Control plants were placed under UV313 bulbs that were covered with polyester (MylarD, US Plastics, Lima, OH, USA), which transmits visible light but excludes UV-B.  After UV irradiation the UV bulbs were turned off and the plants were allowed to recover for 4 h in the greenhouse.  The second and third seedling leaf from each of four plants was harvested and dropped immediately into liquid nitrogen.  Pooling assured sufficient RNA and also decreases biological variability.  Total RNA was extracted from frozen tissue using Trizol (Invitrogen Co., Carlsbad, CA), as described in the microarray manufacturer’s protocol (http://www.zmdb.iastate.edu/zmdb/microarray/protocols.html#P3).  PolyA-plus messenger RNA was prepared from the total RNA using a Qiagen Oligotex kit (Qiagen Corp., Valencia, CA).  Poly(A)+ RNA was isolated using Oligotex (Qiagen Inc., Valencia, CA), and 4 mg of poly (A)+ RNA was used for each cDNA synthesis using Superscript II reverse transcriptase (Life Technologies, Carlsbad, CA).  cDNA was labeled using 100 mM Cy5-dUTP or Cy3-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ).  Excess nucleotides and primers were removed using QIAquick PCR Purification Kit (Qiagen, Valencia, CA).  About 95% of the spotted cDNAs showed significant hybridization when leaf mRNA was used for the experiments.  The control sample was labeled with Cy5-dUTP fluorescent dye and the UV treatment sample was labeled with Cy3-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ, USA).  Two samples, one labeled with each dye, were mixed and then hybridized to a microarray for 15 h at 60°C.  The slides were washed in three wash steps: 2x SSC, 0.5% SDS; 0.5x SSC; and 0.05x SSC.  The three washes were at room temperature for 5 min each with gentle shaking.  The slides were scanned with a GenePix 4000B Scanner (Axon Instruments Inc., Union City, CA).  Normalization between the Cy3 and Cy5 fluorescent dye emission channels was achieved by adjusting the levels of both image intensities.  Scanalyze (Eisen, http://rana.lbl.gov/EisenSoftware.htm) was used to quantify the image files from the scanner.
Keywords = ultraviolet maize corn seedling leaf

molecule: total RNA

organism: Zea mays

source_name: B73 seedling leaf2and3 ultraviolet treatment

source_name: B73 seedling leaf2and3 control


title: Mo17Ch1greenUV1

source_name: Mo17 seedling leaf2and3 ultraviolet treatment

source_name: Mo17 seedling leaf2and3 control


title: Mo17Ch1greenControl1

description:
Inbred lines B73 and Mo17, from the same stocks used to create the IBM mapping lines, were kindly supplied by M. Lee.  These lines were increased in the field nursery at Clayton, NC. Individual seeds were placed one per 6 cm pot filled with vermiculite, at a density of 36 pots per flat, and grown in the greenhouse without supplemental lighting for ten days to the two-leaf stage.  The greenhouse photosynthetically active radiation levels are ~20% less than outdoor radiation.  The two lines were then exposed to 4 h of ultraviolet radiation from UV313 bulbs (Q Panel, Westlake, OH, USA) suspended about 30 cm above the plants.  The UV dose was measured at plant height using the UV-B sensor on an International Light radiometer Model IL1400A (International Light, Newburyport, MA); the treatment plants received a total UV dose of 86 Jm-2.  Control plants were placed under UV313 bulbs that were covered with polyester (MylarD, US Plastics, Lima, OH, USA), which transmits visible light but excludes UV-B.  After UV irradiation the UV bulbs were turned off and the plants were allowed to recover for 4 h in the greenhouse.  The second and third seedling leaf from each of four plants was harvested and dropped immediately into liquid nitrogen.  Pooling assured sufficient RNA and also decreases biological variability.  Total RNA was extracted from frozen tissue using Trizol (Invitrogen Co., Carlsbad, CA), as described in the microarray manufacturer’s protocol (http://www.zmdb.iastate.edu/zmdb/microarray/protocols.html#P3).  PolyA-plus messenger RNA was prepared from the total RNA using a Qiagen Oligotex kit (Qiagen Corp., Valencia, CA).  Poly(A)+ RNA was isolated using Oligotex (Qiagen Inc., Valencia, CA), and 4 mg of poly (A)+ RNA was used for each cDNA synthesis using Superscript II reverse transcriptase (Life Technologies, Carlsbad, CA).  cDNA was labeled using 100 mM Cy5-dUTP or Cy3-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ).  Excess nucleotides and primers were removed using QIAquick PCR Purification Kit (Qiagen, Valencia, CA).  About 95% of the spotted cDNAs showed significant hybridization when leaf mRNA was used for the experiments.  The control sample was labeled with Cy3-dUTP fluorescent dye and the UV treatment sample was labeled with Cy5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ, USA).  Two samples, one labeled with each dye, were mixed and then hybridized to a microarray for 15 h at 60°C.  The slides were washed in three wash steps: 2x SSC, 0.5% SDS; 0.5x SSC; and 0.05x SSC.  The three washes were at room temperature for 5 min each with gentle shaking.  The slides were scanned with a GenePix 4000B Scanner (Axon Instruments Inc., Union City, CA).  Normalization between the Cy3 and Cy5 fluorescent dye emission channels was achieved by adjusting the levels of both image intensities.  Scanalyze (Eisen, http://rana.lbl.gov/EisenSoftware.htm) was used to quantify the image files from the scanner.
Keywords = ultraviolet maize corn seedling leaf


title: B73Ch1greencontrol1

description:
Inbred lines B73 and Mo17, from the same stocks used to create the IBM mapping lines, were kindly supplied by M. Lee.  These lines were increased in the field nursery at Clayton, NC. Individual seeds were placed one per 6 cm pot filled with vermiculite, at a density of 36 pots per flat, and grown in the greenhouse without supplemental lighting for ten days to the two-leaf stage.  The greenhouse photosynthetically active radiation levels are ~20% less than outdoor radiation.  The two lines were then exposed to 4 h of ultraviolet radiation from UV313 bulbs (Q Panel, Westlake, OH, USA) suspended about 30 cm above the plants.  The UV dose was measured at plant height using the UV-B sensor on an International Light radiometer Model IL1400A (International Light, Newburyport, MA); the treatment plants received a total UV dose of 86 Jm-2.  Control plants were placed under UV313 bulbs that were covered with polyester (MylarD, US Plastics, Lima, OH, USA), which transmits visible light but excludes UV-B.  After UV irradiation the UV bulbs were turned off and the plants were allowed to recover for 4 h in the greenhouse.
The second and third seedling leaf from each of four plants was harvested and dropped immediately into liquid nitrogen.  Pooling assured sufficient RNA and also decreases biological variability.  Total RNA was extracted from frozen tissue using Trizol (Invitrogen Co., Carlsbad, CA), as described in the microarray manufacturer’s protocol (http://www.zmdb.iastate.edu/zmdb/microarray/protocols.html#P3).  PolyA-plus messenger RNA was prepared from the total RNA using a Qiagen Oligotex kit (Qiagen Corp., Valencia, CA).  Poly(A)+ RNA was isolated using Oligotex (Qiagen Inc., Valencia, CA), and 4 mg of poly (A)+ RNA was used for each cDNA synthesis using Superscript II reverse transcriptase (Life Technologies, Carlsbad, CA).  cDNA was labeled using 100 mM Cy5-dUTP or Cy3-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ).  Excess nucleotides and primers were removed using QIAquick PCR Purification Kit (Qiagen, Valencia, CA).  About 95% of the spotted cDNAs showed significant hybridization when leaf mRNA was used for the experiments.  The control sample was labeled with Cy3-dUTP fluorescent dye and the experimental UV-treated sample with Cy5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ, USA).  Two samples, one labeled with each dye, were mixed and then hybridized to a microarray for 15 h at 60°C.  The slides were washed in three wash steps: 2x SSC, 0.5% SDS; 0.5x SSC; and 0.05x SSC.  The three washes were at room temperature for 5 min each with gentle shaking.  The slides were scanned with a GenePix 4000B Scanner (Axon Instruments Inc., Union City, CA).  Normalization between the Cy3 and Cy5 fluorescent dye emission channels was achieved by adjusting the levels of both image intensities.  Scanalyze (Eisen, http://rana.lbl.gov/EisenSoftware.htm) was used to quantify the image files from the scanner.


title: CDC5328

status: Public on Jan 24 2008

type: genomic

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

description: GFF file shows signal intensities for both channels.

hyb_protocol: Arrays were co-hybridized with both Cy3-labeled DNA (Test strain) and Cy5-labeled DNA (reference strain) for 14 hours at 42C.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner at 532nm and 635 nm.

data_processing: Signal intensities were extracted and normalized log2 ratio data were determined using Nimblescan v. 2.3 software (Nimblegen).

molecule: genomic DNA

organism: Clostridium botulinum

label_protocol: 1 ug of genomic DNA was labeled with Cy3 random primers and Klenow fragment

extract_protocol: Epicenter MasterPure DNA Purification Kit (Madison, WI)

tag: strain

source_name: ATCC 3502

label_protocol: 1 ug of genomic DNA was labeled with Cy5 random primers and Klenow fragment


title: Mo17Ch1greenControl2


title: CDC1882


title: CDC51303


title: CDC21547


title: CDC1903


title: CDC297


title: FRI-H1A2


title: NHGRI Ink4a-a/a mv31939 (20071214)

status: Public on May 04 2009

city: Bethesda

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

description: Ink4a-a/a vs Universal reference

hyb_protocol: The combined Cy3 and Cy5 labeled cDNAs are put in a total volume of 250 ul DEPC H20 and 250 ul of 2X Agilent hybridization buffer. The mixture is then denatured for 2 minutes and applied on the Agillent hybridization chamber/gasket slide in sandwich with the array slide. The hybridization is performed at 65 degre for 16 hours.

scan_protocol: Agilent Scanner

data_processing: IPLab/DeArray software, lowess normalization

organism: Mus musculus

label_protocol: 10-15 microgram of total RNA was reverse transcribed with Anchor Oligo-dT and Aminoallyl dUTP, after NaOH RNA hydrolysis, the labeled Aminoallyl dUTP cDNA is purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104). The Aminoallyl dUTP cDNAs are then coupled with either Cy3 or Cy5 mono NHS Ester Dyes. The CyDyes labeled cDNAs are then purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104).

extract_protocol: RNA was extracted with Trizol/Chloroform method according to manifecturer protocol and the RNA is further purified by the Qiagen RNAeazy columns

tag: C57BL/6 melan Ink4a-1 melanocyte line

source_name: Stratagene Universal Mouse Reference RNA

extract_protocol: not applicable

tag: StratageneÕs Universal Mouse Reference RNA is a high-quality control for mouse-based microarray experiments that has quickly become an industry standard for mouse microarray experiments (see citation database). Comprised as a collection of RNA pooled from eleven cell lines


title: MouseMG_MMTV-CRE;SOX9+/F_REP1

status: Public on May 02 2009

city: Worcester

first: Shaolei

last: Lu

state: MA

address: 364 Plantation Street

department: Cancer Biology

institute: University of Massachusetts Medical School

description: UMASS MED GENOMICS CORE PROTOCOL

hyb_protocol: UMASS MED GENOMICS CORE PROTOCOL

scan_protocol: UMASS MED GENOMICS CORE PROTOCOL

data_processing: PLIER EXPRESSION CONSOLE 1.0

label: UMASS MED GENOMICS CORE PROTOCOL

source_name: MouseMG_MMTV-CRE;SOX9+/F R35

label_protocol: UMASS MED GENOMICS CORE PROTOCOL

growth_protocol: ROUTINE MAINTENANCE

extract_protocol: QIAGEN RNEASY MINI KIT

treatment_protocol: VIRGIN MICE, NO TREATMENT

value: C57BL/6 X FVB

tag: gender

value: FEMALE

tag: age

value: 5 WKS

tag: tissue

value: MAMMARY GLAND

tag: genotype

tag: tissue id


title: Human cerebellum, pooled, technical rep 3

status: Public on May 05 2009

city: Iowa City

first: Yi

last: Xing

state: IA

address: 3294 CBRB, 285 Newton Rd

department: Internal Medicine, Biomedical Engineering

institute: University of Iowa

hyb_protocol: The labeling assay yielded labeled single-stranded DNA that was fragmented and hybridized to Affymetrix Human Exon Junction arrays (HJAY arrays) according to manufacturer’s protocols at the University of Iowa DNA facility.

scan_protocol: Hybridized Affymetrix Human Exon Junction arrays (HJAY arrays) were scanned following the manufacturer’s protocols at the University of Iowa DNA facility.

data_processing: Raw image files were processed using Affymetrix GCOS software to generate CEL data files. The GeneBASE algorithm (Kapur et al., 2007, Genome Biol 8:R82) was used to produce the expression values, with minor modifications. Exon array expression indexes were calculated by the JETTA program using perfect-match probes shared between human, chimpanzee and rhesus macaque genomes.

label: biotin

organism: Homo sapiens

source_name: human cerebellum

label_protocol: Biotinylated sense-strand DNA for hybridization to Affymetrix Human Exon Junction arrays (HJAY arrays) was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).  Ribosomal RNA reduction was performed using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, K1550-01).

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions. RNA was quantified (A260) using a Nanodrop-1000 spectrophotometer (Nanodrop Technologies).

value: cerebellum (pooled from 24 donors)

value: male/female

value: 16-70 years


title: clear cell RCC kidney tumor sample, biological rep1

status: Public on Apr 28 2009

city: Boston

first: Hasan

middle: Huseyin

last: Otu

address: 4 Blackfan Circle Rm. 238

department: Medicine

institute: Harvard Medical School

description: Affymetrix HG-U133A gene expression data from clear cell RCC kidney tumor sample.

hyb_protocol: Following fragmentation, ~5 microg of cRNA were hybridized for 16 hr at 45C on Human Genome 133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The data in the Sample table were analyzed with dChip using smoothing spline invariant set method with the model based expression algorithm following the perfect match (PM)-mismatch (MM) difference model. In the dChip analysis, array outliers are not treated as missing expression values and no truncation on signal values is applied.

Signal values from a MAS5 analysis are available in the 'GSE15641_mas5_data.txt' file, which is linked to the GSE15641 record as as supplementary file.

source_name: cancerous human kidney tissue, clear cell RCC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from ~5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Kidney


title: LP seedling Bio rep1_A Rep 1 RicechipA

status: Public on Apr 22 2009

city: Beijing

first: lihuang

last: Zhu

address: Datun Road, Chaoyang District,100101 Beijing China

department: Plant Gene Research Center

country: China

institute: The Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences (CAS)

description: One biological replication unit coming from pools of 3~6 individual samples

hyb_protocol: 42C 50% formamide

scan_protocol: Packard Scanarray Lite

data_processing: For each slide, spots flagged bad by Genepix were removed from the latter analysis step. Then based on the spot signals distribution of positive and negative controls among hybridization data, the threshold for expression was determined with false positive below 5%, only those genes expressed at least two independent replications were kept for further analysis. The filtered data set was normalized based on the median of all expressed genes to normalize the intensity of different experiments, and normalization of two channels of each array was done using intensity-based loess method with R language.

organism: Oryza sativa

source_name: LYP9,seedling, shoot

label_protocol: amino-allyl and monofunctional dye

extract_protocol: Guanidinium Isothiocyanate(Molecular cloning III)

value: the green part

tag: development stage

value: 7 days old

tag: environment

value: culture room

source_name: PA64s,seedling, shoot